##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CatsCradle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CatsCradle_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CatsCradle/DESCRIPTION’ ... OK
* this is package ‘CatsCradle’ version ‘1.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CatsCradle’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
edgeLengthPlot: no visible binding for global variable ‘cellTypePair’
edgeLengthPlot: no visible binding for global variable ‘cutoff’
make.getExample : getExample: no visible binding for global variable
  ‘seuratGenes’
make.getExample : getExample: no visible binding for global variable
  ‘seuratCells’
make.getExample : getExample: no visible binding for global variable
  ‘xeniumCells’
make.getExample : getExample: no visible binding for global variable
  ‘moransI’
make.getExample : getExample: no visible binding for global variable
  ‘moransILigandReceptor’
make.getExample : getExample: no visible binding for global variable
  ‘humanLRN’
make.getExample : getExample: no visible binding for global variable
  ‘mouseLRN’
meanGeneClusterOnCellUMAP: no visible binding for global variable
  ‘UMAP_1’
meanGeneClusterOnCellUMAP: no visible binding for global variable
  ‘UMAP_2’
Undefined global functions or variables:
  UMAP_1 UMAP_2 cellTypePair cutoff humanLRN moransI
  moransILigandReceptor mouseLRN seuratCells seuratGenes xeniumCells
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'aggregateGeneExpression.Rd':
aggregateGeneExpression
  Code: function(f, neighbourhoods, self = FALSE, verbose = TRUE,
                 returnType = "Seurat")
  Docs: function(f, neighbourhoods, verbose = TRUE, returnType =
                 "Seurat")
  Argument names in code not in docs:
    self
  Mismatches in argument names:
    Position: 3 Code: self Docs: verbose
    Position: 4 Code: verbose Docs: returnType

Codoc mismatches from Rd file 'nbhdsAsEdgesToNbhdsAsList.Rd':
nbhdsAsEdgesToNbhdsAsList
  Code: function(cells, neighbourhoods, self = FALSE)
  Docs: function(cells, neighbourhoods)
  Argument names in code not in docs:
    self

* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'getFeatureZScores.Rd'
  ‘features’
Documented arguments not in \usage in Rd file 'getFeatureZScores.Rd':
  ‘featurs’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
randomiseNodeIndices                30.846  0.263  31.705
computeNBHDVsCTObject               26.204  0.211  26.634
getObjectSubsetClusteringPValue     22.504  0.882  23.574
aggregateGeneExpression             20.256  0.608  21.269
computeGraphEmbedding               14.174  0.148  14.453
predictAnnotation                   13.356  0.884  14.380
transposeObject                     12.632  0.106  12.983
predictAnnotationAllGenes           11.734  0.440  12.449
edgeCutoffsByZScore                  9.723  0.527  10.382
predictGeneAnnotationImpl            9.412  0.495  10.061
cullEdges                            9.404  0.442  10.073
performLigandReceptorAnalysis        7.296  2.090   9.661
edgeCutoffsByClustering              8.698  0.552   9.337
edgeLengthsAndCellTypePairs          8.800  0.446   9.722
edgeCutoffsByWatershed               8.809  0.431   9.734
edgeLengthPlot                       8.693  0.543   9.432
edgeCutoffsByPercentile              8.620  0.473   9.203
collapseExtendedNBHDs                7.958  0.081   8.149
combinatorialSpheres                 7.594  0.106   7.793
medianComplementPValue               7.534  0.089   8.269
runGeometricClusteringTrials         7.484  0.134   7.678
getObjectSubsetClusteringStatistics  7.310  0.097   7.474
getNearbyGenes                       7.301  0.079   7.456
tagRowAndColNames                    7.247  0.088   7.473
geneSetsVsGeneClustersPValueMatrix   7.218  0.104   7.608
getAverageExpressionMatrix           7.139  0.076   7.321
getAverageExpressionDF               7.093  0.064   7.222
desymmetriseNN                       6.672  0.098   6.909
meanZPerClusterOnUMAP                6.638  0.053   6.955
getGeneNeighbors                     6.479  0.083   6.705
meanZPerCluster                      6.475  0.064   6.706
symmetryCheckNN                      6.456  0.066   6.594
meanGeneClusterOnCellUMAP            6.419  0.062   6.612
getClusterOrder                      6.310  0.084   6.521
getGeneClusterAveragesPerCell        6.287  0.076   6.411
getNearestNeighbourLists             6.261  0.056   6.396
symmetriseNN                         6.150  0.087   6.415
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CatsCradle.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CatsCradle
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘CatsCradle’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CatsCradle)